Jose Rodriguez has no regrets about the CIA using "enhanced interrogation techniques" -- methods that some consider torture - on suspected al Qaeda members detained and questioned after 9/11. Lesley Stahl interviews the former head of the CIA's Clandestine Service about waterboarding and other methods he says were essential to getting information from suspected terrorists, and he denies claims that these harsh measures caused detainees to provide false or unreliable information that misled the CIA. In fact, Rodriguez says that high-level detainees Khalid Sheik Mohammed and Abu Zubaydah provided their best information only after harsh treatment, a claim that the CIA's own investigator general has challenged.

The following script is from "Hard Measures" which originally aired on April 29, 2012. Lesley Stahl is the correspondent. Richard Bonin, producer.

After the attacks of 9/11, the CIA sought and was granted unprecedented authority to capture al Qaeda suspects, whisk them off to secret sites and interrogate them with harsh techniques, including waterboarding.

The man who ran the interrogation program was Jose Rodriguez, a CIA spy in Latin America, who rose to become head of the Clandestine Service, the CIA's dark side.

When the agency's secret program was revealed, it was widely criticized but the blunt-spoken, Puerto Rican-born Rodriguez is fighting back. He's written a book, a defense of the interrogations, called "Hard Measures" -- and tonight you will hear his side of the story.

It's the first time someone this close to the program, this accountable has gone public explaining why techniques that had long been condemned by the U.S. as torture were employed.

Jose Rodriguez: For the first time in our history, we had an enemy come into our homeland and kill 3,000 people. I mean, that was a huge deal. People jumping from the towers to their death. The people running away from the cloud of dust, terrified out of their mind. This was a threat. And we had to throw everything at it.

Which is why Jose Rodriguez says that when he ran the CIA's Counterterrorist Center, he came up with the idea of employing harsh interrogation techniques. And10 years later, he feels he still has to justify their use.

Lesley Stahl: You had no qualms? We used to consider some of them war crimes.

Jose Rodriguez: We made some al Qaeda terrorists with American blood on their hands uncomfortable for a few days. But we did the right thing for the right reason. And the right reason was to protect the homeland and to protect American lives. So yes, I had no qualms.

Rodriguez spent 31 years in the CIA's Clandestine Service where spies are revered as "fighter jocks". He rose thru the ranks, eventually running covert operations as head of the Latin America division. When al Qaeda struck on 9/11, he'd had no experience in counterterrorism or the Middle East. But he wanted "in" on the war on terror, and went to the CIA's Counterterrorist Center, where the main objective was to stop another attack on the U.S. homeland.

Jose Rodriguez: We were flooded with intelligence about an imminent attack. That al Qaeda had an anthrax program, and that they were planning to use it against us. And that they were seeking nuclear materials to use in some type of nuclear weapon. So we were facing a ticking, time bomb situation and we were very concerned.

Lesley Stahl: So you were getting pressure from Congress and the White House to take the gloves off. Did you go to the dark side?

Jose Rodriguez: Well, the dark side, that's what we do.

Lesley Stahl: You are the dark side.

Jose Rodriguez: We are the dark side.

His first big operation came after the capture of a Palestinian, thought then to have high level al Qaeda connections, named Abu Zubaydah when he was taken prisoner in Pakistan in the spring of 2002, Abu Zubaydah was badly injured in a firefight.

Jose Rodriguez: He actually was on the verge of dying. So we brought in a surgeon from the U.S. to help him out.

Lesley Stahl: You brought in a top-rate surgeon from Johns Hopkins?

Jose Rodriguez: Yes, the best that we could find.

Lesley Stahl: You save him so you can squeeze everything out of his brain that you can?

Jose Rodriguez: So we could elicit intelligence that would allow us to keep our country safe. So we took him to a black site.

Black site. It was the first of several secret interrogation centers around the world. Abu Zubaydah was still recovering from his gunshot wounds when the interrogation began.

Lesley Stahl: When you start the interrogation, it's both the CIA and the FBI, right?

Jose Rodriguez: Correct. This was our prisoner, our site, our show -

Lesley Stahl: Meaning the CIA?

Jose Rodriguez: The CIA, but we had invited the FBI to come along.

Now there's a big dispute over which agency got more information and more valuable information. At first, FBI interrogators used their standard interviewing techniques with no coercion, and Abu Zubaydah cooperated, giving tips and leads but--

Jose Rodriguez: After he regains his strength he stopped talking.

Lesley Stahl: And then he just shuts down. Is that what happens?

Jose Rodriguez: He shuts down.

But the FBI's lead interrogator said he didn't shut down, and that they should continue with their traditional methods of questioning. Jose Rodriguez, though heard the ticking time bomb and felt a sense of urgency.

Jose Rodriguez: If there was going to be another attack against the U.S., we would have blood on our hands because we would not have been able to extract that information from him. So we started to talk about an alternative set of interrogation procedures.

Lesley Stahl: So you're the one who went looking for something to break this guy.

Jose Rodriguez: Yes. And let me tell you something, you know, because years later the 9/11 Commission accused, or said that 9/11 was a failure of imagination. Well, there was no lack of imagination on the part of the CIA in June 2002. We were looking for different ways of doing this.

His search led him to a former military psychologist who had helped train American soldiers in how to resist torture if they were captured. The psychologist adapted the brutal tactics of our Cold War adversaries into what the CIA called "enhanced interrogation techniques." A team of interrogators -- about six of them -- was given a two-week training course and while Jose Rodriguez himself never engaged in any of the sessions with detainees, he supervised the program.

Lesley Stahl: Did the psychologist, did he tell you how long it was going to take, if you use these techniques, to break Abu Zubaydah and anybody else that you might capture?

Jose Rodriguez: You know, he had speculated that within 30 days we would probably be able to get the information that we wanted, yes.

But before moving forward, Jose Rodriguez got his superiors, right up to the president - to sign off on a set of those techniques, including waterboarding.

Jose Rodriguez: We needed to get everybody in government to put their big boy pants on and provide the authorities that we needed.

Lesley Stahl: Their big boy pants on--

Jose Rodriguez: Big boy pants. Let me tell you, I had had a lot of experience in the agency where we had been left to hold the bag. And I was not about to let that happen for the people that work for me.

Lesley Stahl: There wasn't gonna be any deniability on this one?

Jose Rodriguez: There was not gonna be any deniability. And I tell you something. In August of 2002, I felt I had all the authorities that I needed, all the approvals that I needed. The atmosphere in the country was different. Everybody wanted us to save American lives.

The authorities came from the Justice Department in an opinion, later dubbed one of "the torture memos" - that detailed what was permissible.

Jose Rodriguez: We went to the border of legality. We went to the border, but that was within legal bounds.

Lesley Stahl: Even after you got the Justice Department legal office to give you this okay, you kept going back and back, with each thing you did. Over and over.

Jose Rodriguez: We wanted to make sure that the rest of government was with us.

Lesley Stahl: How does the water boarding that you engaged in, how did that work?

Jose Rodriguez: The detainee was strapped to an inclined board with his feet up so that no water would go--

Lesley Stahl: So his head was back.

Jose Rodriguez: So his head was back. And a cloth was placed over the mouth and nose. And water was applied to it.

Lesley Stahl: Oh he couldn't breathe through his nose.

Jose Rodriguez: So when he was saturated, then the air flow would be stopped.

Lesley Stahl: And he'd have the sensation of drowning.

Jose Rodriguez: And he would have the sensation.

Lesley Stahl: And was he naked?

Jose Rodriguez: In many cases, nudity was used extensively. And it worked well.

Lesley Stahl: Why is nudity effective?

Jose Rodriguez: It is effective because a lot of people feel very vulnerable when they're nude. And also because of the culture. Nudity, it is not something that is common.

Each step they took was specifically spelled out in the Justice Department memo. For instance, uncooperative detainees could be put in a small, dark: "cramped confinement box with an insect" in it. As for waterboarding, the interrogators were allowed to pour water for up to 40 seconds at a time... quote applied "from a height of 12 to 24 inches"... using about a liter of water per session.

Lesley Stahl: Oh, you had rules for each thing?

Jose Rodriguez: Yes, we had rules. And not only that, but every time we did any of this, we had to ask permission. The field had to ask permission of headquarters.

Lesley Stahl: Each time.

Jose Rodriguez: Each time.

Lesley Stahl: Each single time...

After Abu Zubaydah was subjected to the CIA's menu of interrogation techniques, Jose Rodriguez says he became compliant in less than three weeks.

Lesley Stahl: Was it waterboarding that broke the dam with Abu Zubaydah?

Jose Rodriguez: I think he was more taken aback by the insult slap.

Lesley Stahl: Oh, what's the insult slap?

Jose Rodriguez: It's just slapping somebody with an open hand so that you don't hurt 'em.

Lesley Stahl: By "hurt," you mean you don't break his jaw?

Jose Rodriguez: We don't break his jaw. And the objective is not to inflict pain. The objective is to let him know there's a new sheriff in town, and he better pay attention.

Lesley Stahl: You also employed stress techniques?

Jose Rodriguez: Uh-huh. There was a technique where the detainee would sit on the floor and would raise his hands over his head.

Lesley Stahl: In other words, he had to hold his hands up there forever and ever, right?

Jose Rodriguez: Forever & ever? I was thinkin' about this the other day. The objective was to induce muscle fatigue, and most people who work out do a lot more fatiguing of the muscles.

Lesley Stahl: Are you saying this was like going to the gym? Come on.

Jose Rodriguez: A little different.

Lesley Stahl: Yeah.

Central to the interrogation was sleep deprivation. Abu Zubaydah was also kept awake for three straight days.

Jose Rodriguez: Sleep deprivation works. I'm sure, Lesley, with all the traveling that you do, that you have suffered from jet lag. And you know, when you don't get a good night's sleep for two, three days, it's very hard.

Lesley Stahl: Now, you don't really mean to suggest that it's like jet lag. I mean, you make it sound like it's benign when you say stuff like that.

Jose Rodriguez: Well, I mean, the feeling--

Lesley Stahl: And you go into the gym and jet lag--

Jose Rodriguez: Well, the feeling that you get when you don't sleep.

Lesley Stahl: But I mean, these were enhanced interrogation techniques. Other people call it torture.This was-- this wasn't benign in any-- any sense of the word.

Jose Rodriguez: I'm not trying to say that they were benign. But the problem is here is that people don't understand that this program was not about hurting anybody. This program was about instilling a sense of hopelessness and despair on the terrorist, on the detainee, so that he would conclude on his own that he was better off cooperating with us.

He says once Abu Zubaydah became compliant, the harsh treatment stopped and he became a fountain of information. But the FBI interrogators remember it differently.

Lesley Stahl: In fact, what they say is everything important that he gave up, he gave up to them before the harsher interrogation techniques kicked in.

Jose Rodriguez: Well, that is just not true. It's not true.

Lesley Stahl: Well, now they say that. And you say, "It's not true." What am I supposed to think? I don't know.

The FBI and CIA disagree and it's impossible for us to resolve the argument because details of the interrogations remain classified. But what about the fact that detainees will say anything to stop the pain.

Lesley Stahl: Here's something that was told to me. Abu Zubaydah's stories sent the CIA around the globe. Not a single plot was foiled. We spent millions chasing phantoms.

Jose Rodriguez: Bullshit. He gave us a road map that allowed us to capture a bunch of Al Qaeda senior leaders.

Among those leaders: Khalid Sheik Mohammed. Details of his interrogation and what he told the CIA. About Osama bin Laden, next.

The CIA had the use of a fleet of special aircraft to spirit detainees to its web of black sites across the globe. They were knocked out with sedatives during the flights and upon arrival had their heads and beards shaved and they were placed in sterile underground cells, with only an arrow painted on the floor pointing to Mecca.

In total, the CIA picked up about 100 detainees, subjected 75 of them to harsh interrogation techniques - three of them to waterboarding, including Khalid Sheikh Mohammed - or KSM, the mastermind of 9/11. When KSM was first captured in 2003, he was in no mood to talk.

Jose Rodriguez: Oh, he was not going to talk. I mean, Khalid Sheik Mohammed is one of the toughest killers out there.

Lesley Stahl: I heard he was brilliant.

Jose Rodriguez: He was brilliant. He was scary smart. But he's also evil. And he will use that intelligence to define different ways of coming after us.

He says that in the beginning, KSM would respond to questions by reciting verses from the Koran.

Jose Rodriguez: He eventually told us, "Well look, I will talk once I get to New York and I get my lawyer." He knew that if he got into the criminal process in the U.S. that he would get a lawyer and he would use that forum.

Lesley Stahl: He'd use it as a platform for his ideology.

Jose Rodriguez: He would use it as a platform.

Faced with KSM's obstinance, CIA interrogators began ratcheting up the severity of the questioning step-by-step.

Lesley Stahl: Did you make him wear diapers?

Jose Rodriguez: Diapers? I don't recall specifically to him. But diapers is something that is approved.

Lesley Stahl: It's so humiliating.

Jose Rodriguez: It's standard. Standard. Yeah.

According to an internal investigation by the CIA's own inspector general - this is a heavily redacted declassified copy. KSM was denied sleep for 180 hours in a row or about seven and a half days. And still he didn't break.

Jose Rodriguez: He was the toughest detainee that we had. No doubt.

So he was subjected to waterboarding, specifically 183 "pourings" of water in about half a dozen separate sessions. Jose Rodriguez said the average pour lasted 10 seconds.

Jose Rodriguez: Can I say something about Khalid Sheikh Mohammed? He's the one that was responsible for the death of Danny Pearl, the Wall Street reporter. He slit his throat in front of a camera. I don't know what type of man it takes to cut the throat of someone in front of you like that, but I can tell you that this is an individual who probably didn't give a rat's ass about having water poured on his face.

Lesley Stahl: He never believed for one second you were going to kill him.

Jose Rodriguez: No. And let me just tell you. Khalid Sheikh Mohammed would use his fingers to count the number of seconds, because he knew that in all likelihood, we would stop at 10. So this doesn't sound like a person who is afraid of dying.

Lesley Stahl: If he's sitting there counting off, he knows you're not going to kill him. He knows he's not going to drown. Then why do it? What's the point?

Jose Rodriguez: Well, I think that the cumulative effect of waterboarding and sleep deprivation and everything else that was done eventually got to him.

Lesley Stahl: So what happens? Does he break down? Does he weep? Does he fall apart?

Jose Rodriguez: No. He gets a good night's sleep. He gets his Ensure. By the way, he was very heavy when he came to us and he lost 50 pounds. So--

Lesley Stahl: What his Ensure? You mean like people in the hospital who drink that stuff?

Lesley Stahl: So sleep deprivation, dietary manipulation. I mean, this is Orwellian stuff. The United States doesn't do that.

Jose Rodriguez: Well, we do.

The question is whether the information they got from KSM was truthful and helpful. In his report, the CIA's inspector general says that the CIA's office of medical services concluded that when it came to the waterboarding--

Lesley Stahl: There was no reason to think that it had been effective or that it was safe. This is your inspector general.

Jose Rodriguez: Well our own inspector general in many cases did very sloppy work. That report is flawed in many different ways.

Lesley Stahl: Why would they make it up?

Jose Rodriguez: I don't know if it's made up. I don't know if they were advocates. You know, the inspector general himself, he was opposed to this. I mean, but this was the policy. So he was wrong.

But many of the tips from detainees reportedly led to blind alleys and expensive wild goose chases. Jose Rodriguez maintains the information from KSM and the other detainees enabled the CIA to disrupt at least 10 large scale terrorist plots.

Lesley Stahl: Would the plots have been stopped without the harsh interrogation techniques? In other words, could it have happened without waterboarding?

Jose Rodriguez: I can't answer that question. Perhaps. But the issue here was timing. We needed information and we needed it right away to protect the homeland.

Lesley Stahl: You told us that the whole rationale, justification for the whole interrogation program was to stop an imminent attack. The inspector general says it didn't stop any imminent attack.

Jose Rodriguez: I submit to you that we don't know. We don't know if, for example, al Qaeda would have been able to continue on with their anthrax program or nuclear program or the second wave of attacks or the sleeper agents that they had inside the United States that were working with Khalid Sheikh Mohammed to take down the Brooklyn Bridge, for example. So, it's easy, years later, to say, "Well, you know, no ticking time bomb-- nothing was stopped."

Lesley Stahl: But the truth is about Khalid Sheikh Mohammed, you really didn't break him.

Jose Rodriguez: Why? Why do you say that?

Lesley Stahl: Well, he didn't tell you about Osama bin Laden. He didn't tell you how to get him. He didn't tell you how to find him.

Jose Rodriguez: Some of these people were not going to tell us everything.

Lesley Stahl: So you don't break 'em.

Jose Rodriguez: There is a limit, there is a limit to what they will tell us.

Actually KSM lied about the courier - whose identity finally led to the compound in Abbottabad, Pakistan, where the terrorist leader he calls Sheikh bin Laden was hiding.

Lesley Stahl: Now, here's what I heard: that Khalid Sheikh Mohammed told you the courier had retired and threw you off the scent for a while.

Jose Rodriguez: That was the one secret he was going to take to the grave, and that was the protection of the Sheikh. He was not going to tell us.

One of the secrets Jose Rodriguez had hoped to take to his grave was exposed in 2007: the CIA had videotaped the interrogation of two of its detainees, including Abu Zubaydah.

Jose Rodriguez: The reason why we taped Abu Zubaydah was because we-- he was very wounded when he was captured. And we feared that he was gonna die in captivity. So we wanted to show the world that we actually had nothing to do with his death. That you know, he died on his own.

Lesley Stahl: Well, that's ironic. You wanted to have a video record that he was being well treated, but in the end they became-- a video record that he had been subjected to these harsh techniques.

Jose Rodriguez: Yeah, we weren't hiding anything.

Lesley Stahl: But you then ordered these tapes destroyed.

Jose Rodriguez: Correct. Ninety-two tapes.

Lesley Stahl: Ninety-two tapes. Why did you order that they be destroyed?

Jose Rodriguez: To protect the people who worked for me and who were at those black sites and whose faces were shown on the tape.

Lesley Stahl: Protect them from what?

Jose Rodriguez: Protect them from al Qaeda ever getting their hands on these tapes and using them to go after them and their families.

He was also worried about the very survival of the CIA's dark side, the Clandestine Service because of the so-called Abu Ghraib effect.

Jose Rodriguez: I was concerned that the distinction between a legally-authorized program as our enhanced interrogation program was, and illegal activity by a bunch of psychopaths would not be made.

He says that CIA lawyers repeatedly asked the White House, Justice Department and Vice President Cheney's office for permission to shred the tapes. But--

Jose Rodriguez: Nobody was making a decision to proceed.

Lesley Stahl: So one day you just said, "The hell with it. I have this authority. I'm going to do it."

Jose Rodriguez: One day I finally called in my advisers and lawyers and say: "Tell me, ok. Tell me again that this is legal. And tell me that I have the authority to do this." When the answer I received was "yes" and "yes," then I said, "Well, I am going to make this decision, and do it myself."

Lesley Stahl: Boom! They were destroyed.

Jose Rodriguez: Yes.

They were destroyed in an industrial-strength shredder.

Lesley Stahl: Here's what you write in your book. You took the president's, the vice president's silence on this to mean they were really relieved that you had taken this on yourself and had done it. That's what you write.

Jose Rodriguez: Correct.

Lesley Stahl: There are people who feel what you did it as a coverup.

Jose Rodriguez: Everything that was on those tapes were authorized activities by the U.S. government. So there was nothing to cover up.

Yet after the story broke in the newspapers, the Justice Department launched a criminal investigation. Ultimately, Jose Rodriguez was cleared of any criminal wrongdoing. By then the CIA's inspector general's report was partly declassified, detailing some of the program's excesses.

Lesley Stahl: Mock executions. People threatened with power drills.

Jose Rodriguez: Yes.

Lesley Stahl: People told that, that you were gonna go and hurt their children, rape their wives.

Jose Rodriguez: Stupid things that were done by people who had no authority to do that.

Lesley Stahl: And they just took it on themselves.

Jose Rodriguez: Correct. And we found out about it and we self-reported, and actually called in the I.G. and said, "You better take a look at what these people did and do what you need to do."

Lesley Stahl: You have some people out there who were taken to black sites. They were subjected to terrible treatment. And they hadn't done anything. I mean they were taken mistakenly. They disappeared. What about them?

Jose Rodriguez: No doubt when you are involved in complicated covert action programs like this one, that some mistakes will be made.

Jose Rodriguez retired from the CIA in January 2008. He has spent the last year writing his book, published by the CBS company Simon and Schuster. In the book he says that by cancelling the interrogation program, President Obama has tied the government's hands in the war on terror.

Jose Rodriguez: We don't capture anybody any more, Lesley. You know their default option of this Administration has been to kill all prisoners. Take no prisoners.

Lesley Stahl: The drones.

Jose Rodriguez: The drones. How could it be more ethical to kill people rather than capture them. I never understood that one.

Lesley Stahl: President Obama has said that what we did was torture.

Jose Rodriguez: Well, President Obama is entitled to his opinion. When President Obama condemns the covert action activities of a previous government, he is breaking the covenant that exists between intelligence officers who are at the pointy end of the spear, hanging way out there, and the government that authorized them and directed them to go there.

Lesley Stahl: John McCain. A huge critic of this program. He had been tortured, so we know where he's coming from. Here's what he said: "It's killing us that America will sink to the level of its worst enemies. We forfeited our values," he said. And I guess what I wanna ask is, didn't it actually change who we are? What we think we're about? I mean, we think we-- we're the country that doesn't do that. Right?

Jose Rodriguez: I am very secure in, in what we did and I am very confident that what we did saved American lives.

This Tuesday is the one-year anniversary of the U.S. Special Forces raid that resulted in the death of Osama bin Laden.